1dan

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
(New page: 100px <applet load="1dan" size="450" color="white" frame="true" align="right" spinBox="true" caption="1dan, 2.00 &Aring; " /> '''Complex Of Active Site Inhibited H...)
Current revision (21:58, 26 March 2025) (edit) (undo)
 
(45 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1dan.gif|left|100px]]
 
-
<applet load="1dan" size="450" color="white" frame="true" align="right" spinBox="true"
 
-
caption="1dan, 2.00 &Aring; " />
 
-
'''Complex Of Active Site Inhibited Human Blood Coagulation Factor Viia With Human Recombinant Soluble Tissue Factor'''<br />
 
-
Bound ligands : [[BGC]],[[CA]],[[CAC]],[[CGU]],[[CH2]],[[CL]],[[DPN]],[[FUC]] <br />
 
-
==Overview==
+
==Complex of active site inhibited human blood coagulation factor VIIA with human recombinant soluble tissue factor==
-
Blood coagulation is initiated when tissue factor binds to coagulation, factor VIIa to give an enzymatically active complex which then activates, factors IX and X, leading to thrombin generation and clot formation. We, have determined the crystal structure at 2.0-A degrees resolution of, active-site-inhibited factor VIIa complexed with the cleaved extracellular, domain of tissue factor. In the complex, factor VIIa adopts an extended, conformation. This structure provides a basis for understanding many, molecular aspects of the initiation of coagulation.
+
<StructureSection load='1dan' size='340' side='right'caption='[[1dan]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
-
==Disease==
+
== Structural highlights ==
-
[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=134390 Coagulation Factor Iii; F3 OMIM:134390]<br />
+
<table><tr><td colspan='2'>[[1dan]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. The March 2006 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Tissue Factor'' by David S. Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2006_3 10.2210/rcsb_pdb/mom_2006_3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DAN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DAN FirstGlance]. <br>
-
[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=227500 Myocardial infarction, decreasedsusceptibility to OMIM:227500]<br />
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2&#8491;</td></tr>
-
 
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=0Z6:D-PHENYLALANYL-N-[(2S,3S)-6-{[AMINO(IMINIO)METHYL]AMINO}-1-CHLORO-2-HYDROXYHEXAN-3-YL]-L-PHENYLALANINAMIDE'>0Z6</scene>, <scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CAC:CACODYLATE+ION'>CAC</scene>, <scene name='pdbligand=CGU:GAMMA-CARBOXY-GLUTAMIC+ACID'>CGU</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene></td></tr>
-
==Gene Ontology Information==
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1dan FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dan OCA], [https://pdbe.org/1dan PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dan RCSB], [https://www.ebi.ac.uk/pdbsum/1dan PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dan ProSAT]</span></td></tr>
-
<table cellpadding='5' width='100%' border='1'>
+
-
<tr><td width=10%>Chain</td><td width=30%>Function</td><td width=30%>Process</td>
+
-
<td width=30%>Component</td></tr><tr><td><b>H, L</b></td><td>[http://ispc.weizmann.ac.il:80/oca-bin/ocaids?idns=go&id=GO:0003802 coagulation factor VIIa acti...]<br>[http://ispc.weizmann.ac.il:80/oca-bin/ocaids?idns=go&id=GO:0004252 serine-type endopeptidase ac...]<br>[http://ispc.weizmann.ac.il:80/oca-bin/ocaids?idns=go&id=GO:0005509 calcium ion binding]<br>[http://ispc.weizmann.ac.il:80/oca-bin/ocaids?idns=go&id=GO:0008233 peptidase activity]<br>[http://ispc.weizmann.ac.il:80/oca-bin/ocaids?idns=go&id=GO:0008236 serine-type peptidase activi...]<br>[http://ispc.weizmann.ac.il:80/oca-bin/ocaids?idns=go&id=GO:0016787 hydrolase activity]<br><td>[http://ispc.weizmann.ac.il:80/oca-bin/ocaids?idns=go&id=GO:0006508 proteolysis]<br>[http://ispc.weizmann.ac.il:80/oca-bin/ocaids?idns=go&id=GO:0007596 blood coagulation]<br><td>[http://ispc.weizmann.ac.il:80/oca-bin/ocaids?idns=go&id=GO:0005576 extracellular region]<br>[http://ispc.weizmann.ac.il:80/oca-bin/ocaids?idns=go&id=GO:0005615 extracellular space]<br></tr>
+
-
<tr><td><b>T, U</b></td><td>[http://ispc.weizmann.ac.il:80/oca-bin/ocaids?idns=go&id=GO:0004872 receptor activity]<br>[http://ispc.weizmann.ac.il:80/oca-bin/ocaids?idns=go&id=GO:0004888 transmembrane receptor activ...]<br>[http://ispc.weizmann.ac.il:80/oca-bin/ocaids?idns=go&id=GO:0004896 hematopoietin/interferon-cla...]<br><td>[http://ispc.weizmann.ac.il:80/oca-bin/ocaids?idns=go&id=GO:0006955 immune response]<br>[http://ispc.weizmann.ac.il:80/oca-bin/ocaids?idns=go&id=GO:0007596 blood coagulation]<br><td>[http://ispc.weizmann.ac.il:80/oca-bin/ocaids?idns=go&id=GO:0005886 plasma membrane]<br>[http://ispc.weizmann.ac.il:80/oca-bin/ocaids?idns=go&id=GO:0016020 membrane]<br>[http://ispc.weizmann.ac.il:80/oca-bin/ocaids?idns=go&id=GO:0016021 integral to membrane]<br></tr>
+
</table>
</table>
 +
== Disease ==
 +
[https://www.uniprot.org/uniprot/FA7_HUMAN FA7_HUMAN] Defects in F7 are the cause of factor VII deficiency (FA7D) [MIM:[https://omim.org/entry/227500 227500]. A hemorrhagic disease with variable presentation. The clinical picture can be very severe, with the early occurrence of intracerebral hemorrhages or repeated hemarthroses, or, in contrast, moderate with cutaneous-mucosal hemorrhages (epistaxis, menorrhagia) or hemorrhages provoked by a surgical intervention. Finally, numerous subjects are completely asymptomatic despite very low factor VII levels.<ref>PMID:8043443</ref> <ref>PMID:2070047</ref> <ref>PMID:1634227</ref> <ref>PMID:8364544</ref> <ref>PMID:8204879</ref> <ref>PMID:7981691</ref> <ref>PMID:7974346</ref> <ref>PMID:8652821</ref> <ref>PMID:8844208</ref> <ref>PMID:8940045</ref> <ref>PMID:8883260</ref> <ref>PMID:9414278</ref> <ref>PMID:9576180</ref> <ref>PMID:9452082</ref> <ref>PMID:11091194</ref> <ref>PMID:11129332</ref> <ref>PMID:10862079</ref> <ref>PMID:12472587</ref> <ref>PMID:14717781</ref> <ref>PMID:19751712</ref> <ref>PMID:18976247</ref> <ref>PMID:19432927</ref> <ref>PMID:21206266</ref> <ref>PMID:21372693</ref>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/FA7_HUMAN FA7_HUMAN] Initiates the extrinsic pathway of blood coagulation. Serine protease that circulates in the blood in a zymogen form. Factor VII is converted to factor VIIa by factor Xa, factor XIIa, factor IXa, or thrombin by minor proteolysis. In the presence of tissue factor and calcium ions, factor VIIa then converts factor X to factor Xa by limited proteolysis. Factor VIIa will also convert factor IX to factor IXa in the presence of tissue factor and calcium.
 +
== Evolutionary Conservation ==
 +
[[Image:Consurf_key_small.gif|200px|right]]
 +
Check<jmol>
 +
<jmolCheckbox>
 +
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/da/1dan_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
 +
<text>to colour the structure by Evolutionary Conservation</text>
 +
</jmolCheckbox>
 +
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1dan ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
Blood coagulation is initiated when tissue factor binds to coagulation factor VIIa to give an enzymatically active complex which then activates factors IX and X, leading to thrombin generation and clot formation. We have determined the crystal structure at 2.0-A degrees resolution of active-site-inhibited factor VIIa complexed with the cleaved extracellular domain of tissue factor. In the complex, factor VIIa adopts an extended conformation. This structure provides a basis for understanding many molecular aspects of the initiation of coagulation.
-
==Related Structures==
+
The crystal structure of the complex of blood coagulation factor VIIa with soluble tissue factor.,Banner DW, D'Arcy A, Chene C, Winkler FK, Guha A, Konigsberg WH, Nemerson Y, Kirchhofer D Nature. 1996 Mar 7;380(6569):41-6. PMID:8598903<ref>PMID:8598903</ref>
-
by [http://bioinfo.tg.fh-giessen.de/pdbselect/README homologous] chain: [http://bip.weizmann.ac.il//oca-bin/ocashort?id=1JPS 1JPS], [http://bip.weizmann.ac.il//oca-bin/ocashort?id=1KLI 1KLI], [http://bip.weizmann.ac.il//oca-bin/ocashort?id=1YGC 1YGC], [http://bip.weizmann.ac.il//oca-bin/ocashort?id=1Z6J 1Z6J]
+
-
==Links==
+
-
[http://ispc.weizmann.ac.il:80/oca-bin/ocashort?id=1DAN 1dan at OCA]<br />
+
-
This structure was featured in Molecule of the Month [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb75_1.html pdb75]<br />
+
-
==References==
+
-
#'''Primary:''' Banner DW, D'Arcy A, Chene C, Winkler FK, Guha A, Konigsberg WH, Nemerson Y, Kirchhofer D "The crystal structure of the complex of blood coagulation factor VIIa with soluble tissue factor." <i>Nature 1996 Mar 7;380(6569):41-6.</i> [http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8598903 PMID:8598903]
+
-
[[Category: D.W.Banner]]
+
-
[[Category: BGC]]
+
-
[[Category: CA]]
+
-
[[Category: CAC]]
+
-
[[Category: CGU]]
+
-
[[Category: CH2]]
+
-
[[Category: CL]]
+
-
[[Category: DPN]]
+
-
[[Category: FUC]]
+
-
[[Category: F3 (Gene)]]
+
-
[[Category: F7 (Gene)]]
+
-
[[Category: Coagulation Factor Iii (Disease)]]
+
-
[[Category: Myocardial infarction (Disease)]]
+
-
[[Category: Homo sapiens]]
+
-
[[Category: H: (SCOP_Domain)]]
+
-
[[Category: L:1-48 (SCOP_Domain)]]
+
-
[[Category: L:49-86 (SCOP_Domain)]]
+
-
[[Category: L:87-142 (SCOP_Domain)]]
+
-
[[Category: T:,U:91-106 (SCOP_Domain)]]
+
-
[[Category: U:107-210 (SCOP_Domain)]]
+
-
[[Category: 49267 (SCOP_Family)]]
+
-
[[Category: 50550 (SCOP_Family)]]
+
-
[[Category: 57201 (SCOP_Family)]]
+
-
[[Category: 57632 (SCOP_Family)]]
+
-
[[Category: 49266 (SCOP_SuperFamily)]]
+
-
[[Category: 50514 (SCOP_SuperFamily)]]
+
-
[[Category: 57197 (SCOP_SuperFamily)]]
+
-
[[Category: 57631 (SCOP_SuperFamily)]]
+
-
[[Category: 48725 (SCOP_Fold)]]
+
-
[[Category: 50493 (SCOP_Fold)]]
+
-
[[Category: 57015 (SCOP_Fold)]]
+
-
[[Category: 57629 (SCOP_Fold)]]
+
-
[[Category: 48724 (SCOP_Class)]]
+
-
[[Category: 56992 (SCOP_Class)]]
+
-
''Page seeded by [http://bip.weizmann.ac.il/oca OCA ] on Thu Oct 25 09:31:08 2007''
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 +
</div>
 +
<div class="pdbe-citations 1dan" style="background-color:#fffaf0;"></div>
 +
 
 +
==See Also==
 +
*[[Factor VIIa|Factor VIIa]]
 +
*[[Factor VIIa 3D structures|Factor VIIa 3D structures]]
 +
*[[Tissue factor|Tissue factor]]
 +
== References ==
 +
<references/>
 +
__TOC__
 +
</StructureSection>
 +
[[Category: Homo sapiens]]
 +
[[Category: Large Structures]]
 +
[[Category: RCSB PDB Molecule of the Month]]
 +
[[Category: Tissue Factor]]
 +
[[Category: Banner DW]]

Current revision

Complex of active site inhibited human blood coagulation factor VIIA with human recombinant soluble tissue factor

PDB ID 1dan

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Personal tools